Aside

Contact Info

Languages

R
Python
Shell/Bash
Git
Docker
Node.js

Packages

Tensorflow
PyTorch
Cuda
LangChain
PEFT
LoRA
Transformers

Publications

Deep learning for detecting and elucidating human T-cell leukemia virus type 1 integration sites (Cell Patterns 2023)

H.Xu* and J.Jia*, H.Jeong,Z.Z

Delineating COVID-19 immunological features using single-cell RNA sequencing (The Innovation 2022)

W.Liu, J.Jia, Y.Dai, W.Chen, G.Pei,Q.Yan, Z.Zhao

Investigating Cellular Trajectories in the Severity of COVID-19 and Their Transcriptional Programs Using Machine Learning Approaches (Genes 2021)

H.Jeong* and J.Jia*, Y.Dai, L.Simon, Z.Zhao

What Controls the Acute Viral Infection Following Yellow Fever Vaccination? (Bulletin of Mathematical Biology 2016)

J.Moore, H.Ahmed, J.Jia, R.Akondy, R.Ahmed, R.Antia

Certificates

Enhancing Data Science Outcomes With Efficient Workflow

NVIDIA

2024

Last updated on 2024-06-11.

Main

Johnathan Jia

Data scientist interested in development and implementation of new deep learning algorithms

Professional Experience

Data Analyst Associate

Baylor College of Medicine

Houston, TX

2023

  • Developed automated pipeline for processing of NGS data with Docker, Python, and R
  • Applied scRNA/snRNA-seq pipelines for mechanistic analysis of transcriptomic data
  • Collaborated with software engineers and clinical geneticists to leverage LLMs for precision diagnosis of rare Mendelian genetic disorders
  • Supervised bioinformatics team to work with collaborators in using algorithms and data to drive hypothesis-driven research conclusions
  • Worked with Dr. Jeong and graduate students to develop mentor-mentee matching tool using LLMs with RAG and RLHF

Graduate Research Assistant

UTHSC Houston Graduate School of Biomedical Sciences

Houston, TX

2022 - 2020

  • Developed a convolutional neural network with self-attention architecture using TensorFlow/Keras libraries to identifying high confidence transcription factor targets for HTLV-1. Available on Github.
  • Performed pseudotime analysis on scRNAseq data to infer which transcription factor programs drive COVID-19 infection severity with Seurat and DriVAER

Research Assistant I

MD Anderson Cancer Center

Houston, TX

2020 - 2019

  • Processed, prepared, and stained patient samples for Nanostring and Cytometry

Education

M.S. in Quantitative Sciences

UTHSC Houston Graduate School of Biomedical Sciences

Houston, TX

2022 - 2020

  • Thesis: DeepHTLV: a deep learning model for detecting and elucidating human T-cell leukemia virus type 1 integration sites

UTHSC Houston McGovern School of Medicine

Houston, TX

2018 - 2015

B.S. in Biology, B.A. in Chemistry

Emory University

Atlanta, GA

2015 - 2011

  • Thesis: Investigating heterogeneity in the dynamics of virus and immune response

Awards

Best Quantitative Sciences Program Seminar Presentation

UTHSC Houston Graduate School of Biomedical Sciences

Houston, TX

2022

First Prize Poster Presentation

UTHSC Houston Graduate School of Biomedical Sciences

Houston, TX

2022

Rheumatology Research Foundation Research Award

UTHSC Houston McGovern School of Medicine

Houston, TX

2016